X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 300.0
Details an equal volume of 7.2 mg/ml Plk4 PB1-PB2 and well solution containing 1.2 M Li2SO4, 100 mM Hepes, pH 7.5 were mixed together and equilibrated over 1 ml of well solution., VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.77 α = 90
b = 135.58 β = 90
c = 46.67 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR scanner 300 mm plate -- 2010-10-01
Diffraction Radiation
Monochromator Protocol
APS ID22 Monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1.00890 APS 22-ID

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.3 31.8 89.3 -- 0.055 -- -- 25256 22051 2.0 2.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.3 2.38 84.7 -- 0.334 3.8 -- 1780

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
SAD 2.3 31.776 -- 0.1 25256 22051 1889 87.31 0.1908 0.1908 0.1847 0.2554 10
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.2995 2.3817 -- 150 1630 0.1981 0.3071 -- 72.0
X Ray Diffraction 2.3817 2.477 -- 173 1819 0.204 0.2938 -- 80.0
X Ray Diffraction 2.477 2.5897 -- 174 1848 0.2095 0.3027 -- 82.0
X Ray Diffraction 2.5897 2.7261 -- 180 1897 0.2111 0.3005 -- 83.0
X Ray Diffraction 2.7261 2.8968 -- 187 2017 0.2128 0.3 -- 88.0
X Ray Diffraction 2.8968 3.1203 -- 197 2106 0.211 0.2954 -- 92.0
X Ray Diffraction 3.1203 3.434 -- 201 2184 0.1944 0.2749 -- 95.0
X Ray Diffraction 3.434 3.9301 -- 206 2144 0.1661 0.2202 -- 93.0
X Ray Diffraction 3.9301 4.9485 -- 207 2224 0.1353 0.1925 -- 95.0
X Ray Diffraction 4.9485 31.7794 -- 214 2293 0.1766 0.2385 -- 92.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -0.3668
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.1324
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.4991
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.072
f_dihedral_angle_d 14.623
f_angle_d 1.09
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3478
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 184

Software

Computing
Computing Package Purpose
sergui Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
Phenix Structure Solution
PHENIX (phenix.refine: 1.6.1_357) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.1_357) refinement
Phenix model building
sergui data collection